1TA2

Crystal structure of thrombin in complex with compound 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.151

Literature

Macromolecules
Sequence Display for 1TA2

Classification: HYDROLASE / HYDROLASE INHIBITOR

Total Structure Weight: 34952.84

Macromolecule Entities
Molecule Chains Length Organism Details
thrombin A 287 Homo sapiens EC#: 3.4.21.5 IUBMB
Fragment: alpha-thrombin
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Hirudin B 11 Hirudo medicinalis Mutation: E362A, Q365A
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
176
Query on 176

A 1-(2-AMINO-3,3-DIPHENYL-PROPIONYL)-PYRROLIDINE- 3-CARBOXYLIC ACID 2,5-DICHLORO-BENZYLAMIDE
C27 H27 Cl2 N3 O2
VTUWWZYFAXSACB-UKILVPOCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
176 Ki: 3 nM (100) BindingDB

Ki: 3 nM  BindingMOAD
Ki: 3 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
TYS
Query on TYS
B L-PEPTIDE LINKING C9 H11 N O6 S TYR

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.151
  • Space Group: C 1 2 1

Unit Cell:

Length (Å) Angle (°)
a = 70.81 α = 90.00
b = 72.36 β = 100.90
c = 72.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-05-19
  • Released Date: 2004-06-08
  • Deposition author(s): Tucker, T.J., Brady, S.F., Lumma, W.C., Lewis, S.D., Gardel, S.J., Naylor-Olsen, A.M., Yan, Y., Sisko, J.T., Stauffer, K.J., Lucas, B.Y., Lynch, J.J., Cook, J.J., Stranieri, M.T., Holahan, M.A., Lyle, E.A., Baskin, E.P., Chen, I.-W., Dancheck, K.B., Krueger, J.A., Cooper, C.M., Vacca, J.P.

Revision History

  • Version 1_0: 2004-06-08

    Type: Initial release

  • Version 1_1: 2008-04-30

    Type: Version format compliance

  • Version 1_2: 2011-07-13

    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance

  • Version 1_3: 2017-10-11

    Type: Refinement description